Insights into modular polyketide synthase loops aided by repetitive sequences
The loops of modular polyketide synthases (PKSs) serve diverse functions but are largely uncharacterized. They frequently contain amino acid repeats resulting from genetic events such as slipped‐strand mispairing. Determining the tolerance of loops to amino acid changes would aid in understanding an...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2021-09, Vol.89 (9), p.1099-1110 |
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| container_title | Proteins, structure, function, and bioinformatics |
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| creator | Hirsch, Melissa Kumru, Kaan Desai, Ronak R. Fitzgerald, Brendan J. Miyazawa, Takeshi Ray, Katherine A. Saif, Nisha Spears, Samantha Keatinge‐Clay, Adrian T. |
| description | The loops of modular polyketide synthases (PKSs) serve diverse functions but are largely uncharacterized. They frequently contain amino acid repeats resulting from genetic events such as slipped‐strand mispairing. Determining the tolerance of loops to amino acid changes would aid in understanding and engineering these multidomain molecule factories. Here, tandem repeats in the DNA encoding 949 modules within 129 cis‐acyltransferase PKSs were cataloged, and the locations of the corresponding amino acids within the module were identified. The most frequently inserted interdomain loop corresponds with the updated module boundary immediately downstream of the ketosynthase (KS), while the loops bordering the dehydratase are nearly intolerant to such insertions. From the 949 modules, no repetitive sequence loop insertions are located within ACP, and only 2 reside within KS, indicating the sensitivity of these domains to alteration. |
| doi_str_mv | 10.1002/prot.26083 |
| format | Article |
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They frequently contain amino acid repeats resulting from genetic events such as slipped‐strand mispairing. Determining the tolerance of loops to amino acid changes would aid in understanding and engineering these multidomain molecule factories. Here, tandem repeats in the DNA encoding 949 modules within 129 cis‐acyltransferase PKSs were cataloged, and the locations of the corresponding amino acids within the module were identified. The most frequently inserted interdomain loop corresponds with the updated module boundary immediately downstream of the ketosynthase (KS), while the loops bordering the dehydratase are nearly intolerant to such insertions. From the 949 modules, no repetitive sequence loop insertions are located within ACP, and only 2 reside within KS, indicating the sensitivity of these domains to alteration.</description><identifier>ISSN: 0887-3585</identifier><identifier>EISSN: 1097-0134</identifier><identifier>DOI: 10.1002/prot.26083</identifier><identifier>PMID: 33843112</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>Acyl Carrier Protein - chemistry ; Acyl Carrier Protein - classification ; Acyl Carrier Protein - genetics ; Acyl Carrier Protein - metabolism ; Acyltransferase ; Acyltransferases - chemistry ; Acyltransferases - classification ; Acyltransferases - genetics ; Acyltransferases - metabolism ; Amino Acid Sequence ; Amino acids ; Bacteria - enzymology ; Bacteria - genetics ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Binding Sites ; biosynthesis ; Cloning, Molecular ; Crystallography, X-Ray ; Dehydration ; Deoxyribonucleic acid ; DNA ; Escherichia coli - genetics ; Escherichia coli - metabolism ; Gene Expression ; Genetic Vectors - chemistry ; Genetic Vectors - metabolism ; Industrial engineering ; Kinetics ; loops ; Manufacturing engineering ; Models, Molecular ; modular polyketide synthase ; Modules ; multidomain protein ; Polyketide synthase ; Polyketide Synthases - chemistry ; Polyketide Synthases - classification ; Polyketide Synthases - genetics ; Polyketide Synthases - metabolism ; Polyketides - chemistry ; Polyketides - metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Recombinant Proteins - chemistry ; Recombinant Proteins - genetics ; Recombinant Proteins - metabolism ; repetitive sequences ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Thermodynamics</subject><ispartof>Proteins, structure, function, and bioinformatics, 2021-09, Vol.89 (9), p.1099-1110</ispartof><rights>2021 Wiley Periodicals LLC.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4483-99e91a15f065b4c88f5abbef28d79728c046f55c68d7462629c04dd19e11fde93</citedby><cites>FETCH-LOGICAL-c4483-99e91a15f065b4c88f5abbef28d79728c046f55c68d7462629c04dd19e11fde93</cites><orcidid>0000-0002-4358-7628</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fprot.26083$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fprot.26083$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33843112$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hirsch, Melissa</creatorcontrib><creatorcontrib>Kumru, Kaan</creatorcontrib><creatorcontrib>Desai, Ronak R.</creatorcontrib><creatorcontrib>Fitzgerald, Brendan J.</creatorcontrib><creatorcontrib>Miyazawa, Takeshi</creatorcontrib><creatorcontrib>Ray, Katherine A.</creatorcontrib><creatorcontrib>Saif, Nisha</creatorcontrib><creatorcontrib>Spears, Samantha</creatorcontrib><creatorcontrib>Keatinge‐Clay, Adrian T.</creatorcontrib><title>Insights into modular polyketide synthase loops aided by repetitive sequences</title><title>Proteins, structure, function, and bioinformatics</title><addtitle>Proteins</addtitle><description>The loops of modular polyketide synthases (PKSs) serve diverse functions but are largely uncharacterized. They frequently contain amino acid repeats resulting from genetic events such as slipped‐strand mispairing. Determining the tolerance of loops to amino acid changes would aid in understanding and engineering these multidomain molecule factories. Here, tandem repeats in the DNA encoding 949 modules within 129 cis‐acyltransferase PKSs were cataloged, and the locations of the corresponding amino acids within the module were identified. The most frequently inserted interdomain loop corresponds with the updated module boundary immediately downstream of the ketosynthase (KS), while the loops bordering the dehydratase are nearly intolerant to such insertions. From the 949 modules, no repetitive sequence loop insertions are located within ACP, and only 2 reside within KS, indicating the sensitivity of these domains to alteration.</description><subject>Acyl Carrier Protein - chemistry</subject><subject>Acyl Carrier Protein - classification</subject><subject>Acyl Carrier Protein - genetics</subject><subject>Acyl Carrier Protein - metabolism</subject><subject>Acyltransferase</subject><subject>Acyltransferases - chemistry</subject><subject>Acyltransferases - classification</subject><subject>Acyltransferases - genetics</subject><subject>Acyltransferases - metabolism</subject><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Bacteria - enzymology</subject><subject>Bacteria - genetics</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Binding Sites</subject><subject>biosynthesis</subject><subject>Cloning, Molecular</subject><subject>Crystallography, X-Ray</subject><subject>Dehydration</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Escherichia coli - 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chemistry</subject><subject>Recombinant Proteins - genetics</subject><subject>Recombinant Proteins - metabolism</subject><subject>repetitive sequences</subject><subject>Sequence Alignment</subject><subject>Sequence Homology, Amino Acid</subject><subject>Substrate Specificity</subject><subject>Thermodynamics</subject><issn>0887-3585</issn><issn>1097-0134</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kctKxDAUhoMoznjZ-ABScCNCNZemTTaCDN5AUWRch7Q9nYl2mpq0St_e6OigLlyFnPPx8R9-hPYIPiYY05PW2e6YpliwNTQmWGYxJixZR2MsRBYzLvgIbXn_hDFOJUs30YgxkTBC6BjdXjfezOadj0zT2Whhy77WLmptPTxDZ0qI_NB0c-0hqq1tfaTDrIzyIXLQBqAzrwGBlx6aAvwO2qh07WH3691Gjxfn08lVfHN3eT05u4mLJBEslhIk0YRXOOV5UghRcZ3nUFFRZjKjosBJWnFepOGfpDSlMkzKkkggpCpBsm10uvS2fb6AsoCmc7pWrTML7QZltVG_N42Zq5l9VSJcngkSBIdfAmdDdt-phfEF1LVuwPZeUU6IkJJKHtCDP-iT7V0TzgsUz0LADLNAHS2pwlnvHVSrMASrj5bUR0vqs6UA7_-Mv0K_awkAWQJvpobhH5W6f7ibLqXvlieerA</recordid><startdate>202109</startdate><enddate>202109</enddate><creator>Hirsch, Melissa</creator><creator>Kumru, Kaan</creator><creator>Desai, Ronak R.</creator><creator>Fitzgerald, Brendan J.</creator><creator>Miyazawa, Takeshi</creator><creator>Ray, Katherine A.</creator><creator>Saif, Nisha</creator><creator>Spears, Samantha</creator><creator>Keatinge‐Clay, Adrian T.</creator><general>John Wiley & Sons, Inc</general><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-4358-7628</orcidid></search><sort><creationdate>202109</creationdate><title>Insights into modular polyketide synthase loops aided by repetitive sequences</title><author>Hirsch, Melissa ; Kumru, Kaan ; Desai, Ronak R. ; Fitzgerald, Brendan J. ; Miyazawa, Takeshi ; Ray, Katherine A. ; Saif, Nisha ; Spears, Samantha ; Keatinge‐Clay, Adrian T.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4483-99e91a15f065b4c88f5abbef28d79728c046f55c68d7462629c04dd19e11fde93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Acyl Carrier Protein - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Proteins, structure, function, and bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hirsch, Melissa</au><au>Kumru, Kaan</au><au>Desai, Ronak R.</au><au>Fitzgerald, Brendan J.</au><au>Miyazawa, Takeshi</au><au>Ray, Katherine A.</au><au>Saif, Nisha</au><au>Spears, Samantha</au><au>Keatinge‐Clay, Adrian T.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Insights into modular polyketide synthase loops aided by repetitive sequences</atitle><jtitle>Proteins, structure, function, and bioinformatics</jtitle><addtitle>Proteins</addtitle><date>2021-09</date><risdate>2021</risdate><volume>89</volume><issue>9</issue><spage>1099</spage><epage>1110</epage><pages>1099-1110</pages><issn>0887-3585</issn><eissn>1097-0134</eissn><abstract>The loops of modular polyketide synthases (PKSs) serve diverse functions but are largely uncharacterized. They frequently contain amino acid repeats resulting from genetic events such as slipped‐strand mispairing. Determining the tolerance of loops to amino acid changes would aid in understanding and engineering these multidomain molecule factories. Here, tandem repeats in the DNA encoding 949 modules within 129 cis‐acyltransferase PKSs were cataloged, and the locations of the corresponding amino acids within the module were identified. The most frequently inserted interdomain loop corresponds with the updated module boundary immediately downstream of the ketosynthase (KS), while the loops bordering the dehydratase are nearly intolerant to such insertions. From the 949 modules, no repetitive sequence loop insertions are located within ACP, and only 2 reside within KS, indicating the sensitivity of these domains to alteration.</abstract><cop>Hoboken, USA</cop><pub>John Wiley & Sons, Inc</pub><pmid>33843112</pmid><doi>10.1002/prot.26083</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-4358-7628</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Acyl Carrier Protein - chemistry Acyl Carrier Protein - classification Acyl Carrier Protein - genetics Acyl Carrier Protein - metabolism Acyltransferase Acyltransferases - chemistry Acyltransferases - classification Acyltransferases - genetics Acyltransferases - metabolism Amino Acid Sequence Amino acids Bacteria - enzymology Bacteria - genetics Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - metabolism Binding Sites biosynthesis Cloning, Molecular Crystallography, X-Ray Dehydration Deoxyribonucleic acid DNA Escherichia coli - genetics Escherichia coli - metabolism Gene Expression Genetic Vectors - chemistry Genetic Vectors - metabolism Industrial engineering Kinetics loops Manufacturing engineering Models, Molecular modular polyketide synthase Modules multidomain protein Polyketide synthase Polyketide Synthases - chemistry Polyketide Synthases - classification Polyketide Synthases - genetics Polyketide Synthases - metabolism Polyketides - chemistry Polyketides - metabolism Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Recombinant Proteins - chemistry Recombinant Proteins - genetics Recombinant Proteins - metabolism repetitive sequences Sequence Alignment Sequence Homology, Amino Acid Substrate Specificity Thermodynamics |
| title | Insights into modular polyketide synthase loops aided by repetitive sequences |
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